Biology subjects

Woods, M. A.

Publications and source records attributed to Woods, M. A..

3 recordsLinked to original sources

bioRxiv2026

Genome-wide Analysis Reveals High Genomic Diversity and Panmixia in Bay Pipefish (Syngnathus leptorhynchus) from Coos Bay, Oregon

The over 300 species of fishes in the charismatic family Syngnathidae (seahorses, pipefish, pipehorses, and seadragons) exhibit remarkable morphological and reproductive adaptations. Most syngnathid species inhabit shallow coastal regions where they are vulnerable to human activities, including habitat degradation and collection for use in traditional medicine and the aquarium trade. A gap remains in our understanding of within-species genetic diversity and population structure for most of the species in this family--information that is crucial for establishing baselines to detect future human-driven changes. Here, we investigate fine-scale population structure and genomic diversity in the bay pipefish (Syngnathus leptorhynchus), one of the relatively few temperate lineages within the Syngnathidae. Bay pipefish are habitat specialists that are closely associated with eelgrass (Zostera marina) along the Pacific coast of North America. Due to the patchy and changing nature of eelgrass habitat, bay pipefish provide an instructive case for using population genomics to explore patterns of connectivity in a dynamic coastal environment. We sampled 116 individuals from two locations separated by approximately 17 km in the Coos Bay estuary (Oregon, USA) and used restriction site-associated DNA sequencing (RAD-seq) to discover high and consistent genetic diversity at both sampling locations, with no indication of inbreeding. Genome-wide patterns of genetic variation showed minimal differentiation between the sampling sites, with levels of divergence indistinguishable from those expected under random sampling. Linkage disequilibrium was low and declined rapidly, and estimates of effective population size indicate a large, well-connected population within Coos Bay. These results establish a crucial genomic baseline for understanding how bay pipefish populations may respond to ongoing changes in their eelgrass habitat and offer a genomic framework for conservation and comparative studies across the Syngnathidae.

evolutionary biology↗

bioRxiv2024

Single Cell RNA Sequencing Provides Clues for the Developmental Genetic Basis of Syngnathidae's Evolutionary Adaptations

Seahorses, pipefishes, and seadragons are fishes from the family Syngnathidae that have evolved extraordinary traits including male pregnancy, elongated snouts, loss of teeth, and dermal bony armor. The developmental genetic and cellular changes that led to the evolution of these traits are largely unknown. Recent syngnathid genome assemblies revealed suggestive gene content differences and provide the opportunity for detailed genetic analyses. We created a single cell RNA sequencing atlas of Gulf pipefish embryos to understand the developmental basis of four traits: derived head shape, toothlessness, dermal armor, and male pregnancy. We completed marker gene analyses, built genetic networks, and examined spatial expression of select genes. We identified osteochondrogenic mesenchymal cells in the elongating face that express regulatory genes bmp4, sfrp1a, and prdm16. We found no evidence for tooth primordia cells, and we observed re-deployment of osteoblast genetic networks in developing dermal armor. Finally, we found that epidermal cells expressed nutrient processing and environmental sensing genes, potentially relevant for the brooding environment. The examined pipefish evolutionary innovations are composed of recognizable cell types, suggesting derived features originate from changes within existing gene networks. Future work addressing syngnathid gene networks across multiple stages and species is essential for understanding how their novelties evolved.

evolutionary biology↗

bioRxiv2020

A simple, cheap, and robust protocol for the identification of mating type in Saccharomyces cerevisiae

Saccharomyces cerevisiae is an exceptional genetic system, with genetic crosses facilitated by its ability to be maintained in haploid and diploid forms. Such crosses are straightforward if the mating type/ploidy of the strains are known. Several techniques can be used to determine mating type (or ploidy), but all have limitations. Here we validate a simple, cheap and robust method to rapidly identify S. cerevisiae mating types. When cells of opposite mating type are mixed in liquid media, they "creep" up the culture vessel sides, a phenotype that can be easily detected visually. In contrast, mixtures of the same mating type or with a diploid simply settle out. The phenotype is robust to different media, cell densities, temperatures and strains, and is observable for several days. Microscopy suggests that cell aggregation during mating is responsible for the phenotype. Yeast knockout collection analysis identified 107 genes required for the creeping phenotype, with these being enriched for mating-specific genes. Surprisingly, the RIM101 signalling pathway was strongly represented. We propose that RIM101 signalling regulates aggregation as part of a wider, previously-unrecognized role in mating. The simplicity and robustness of this method makes it ideal for routine verification of S. cerevisiae mating type, with future studies required to verify its molecular basis.

microbiology↗